| T7 |
| ID: | 1446761327 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 53 (53) | ||
| Sequences: | 195 (103.7) | ||
| Seq/Len: | 3.679 | ||
| Nf(neff/√len): | 14.2 |
HHblits Results: (2015_06)
Sequences per length for each position, BEFORE the coverage/gap filter was applied
Legend: Dots above the red line, indicates positions where there is > 5 sequences per length (if visible, green bar = 20 seq/len). Point of this graphic is to give you an idea if resubmitting a sub-portion of your sequence might help increase the overall Seq/Len (which after applying the coverage filter is at: 3.679).
Sequences per length for each position, AFTER the coverage/gap filter was applied
Residue pairs sorted by coevolution strength:
Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] covarying residues with sequence seperation > 3. The i and j are positions as given in the input sequence.
| i | j | Scaled score | Prob |
| 49_L | 53_S | 1.788 | 0.99 |
| 4_L | 8_S | 1.774 | 0.99 |
| 13_G | 16_I | 1.728 | 0.99 |
| 5_S | 9_K | 1.702 | 0.99 |
| 48_L | 51_P | 1.664 | 0.99 |
| 7_E | 11_R | 1.561 | 0.98 |
| 27_Y | 31_I | 1.461 | 0.96 |
| 9_K | 27_Y | 1.392 | 0.95 |
| 9_K | 31_I | 1.375 | 0.95 |
| 23_V | 49_L | 1.365 | 0.94 |
| 25_Y | 39_S | 1.308 | 0.92 |
| 39_S | 43_P | 1.251 | 0.90 |
| 13_G | 32_L | 1.229 | 0.89 |
| 20_R | 25_Y | 1.226 | 0.89 |
| 11_R | 15_L | 1.222 | 0.89 |
| 43_P | 51_P | 1.208 | 0.88 |
| 30_L | 41_P | 1.196 | 0.87 |
| 37_T | 42_R | 1.152 | 0.84 |
| 21_V | 24_H | 1.110 | 0.81 |
| 27_Y | 40_V | 1.102 | 0.81 |
| 19_S | 23_V | 1.092 | 0.80 |
| 6_E | 9_K | 1.088 | 0.79 |
| 49_L | 52_L | 1.074 | 0.78 |
| 17_D | 20_R | 1.066 | 0.77 |
| 10_E | 21_V | 1.051 | 0.76 |
| 2_F | 44_S | 1.049 | 0.76 |
| 48_L | 53_S | 1.042 | 0.75 |
| 10_E | 13_G | 1.023 | 0.73 |
| 38_R | 41_P | 1.023 | 0.73 |
| 50_S | 53_S | 1.022 | 0.73 |
| 1_M | 38_R | 1.016 | 0.72 |
| 34_L | 45_I | 1.006 | 0.71 |
Prob = P(contact | scaled_score, seq/len).
Scaled Score = (raw_score/average(raw_scores)).
- Text file of contact predictions (all 3L/2 predictions)
- Generate restraints for ROSETTA Structure Modeling
- Import to GREMLIN BETA - features includes ability to upload PDB and latest P(contact) calculation based on eLife 2015 fitting to PDB data.
GREMLIN results overlayed on top 10 PDB hits:
Legend: Blue filled circles are GREMLIN results (Scaled Score > 1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 HHsearch results which uses the overall probability and per-position alignment confidence. Inter oligomeric contacts in the pdb are in shades of red.
| PDB | M | Cov | P(%) | HHΔ | |
| 2wswA | 1 | 0.9623 | 61.4 | 0.822 | Contact Map |
| 4c7rA | 3 | 0.9245 | 39.9 | 0.843 | Contact Map |
| 4cr2Z | 1 | 0.9623 | 15.7 | 0.871 | Contact Map |
| 4h63H | 1 | 0.7736 | 6.8 | 0.891 | Contact Map |
| 4oudA | 1 | 0.9623 | 6.4 | 0.892 | Contact Map |
| 4x2uA | 1 | 0.3396 | 6.3 | 0.893 | Contact Map |
| 4eljA | 1 | 0.9623 | 5.9 | 0.894 | Contact Map |
| 1f08A | 2 | 0.9811 | 5.1 | 0.897 | Contact Map |
| 4ly8A | 4 | 0.4528 | 5.1 | 0.897 | Contact Map |
| 4kriA | 3 | 0.8302 | 5.1 | 0.897 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)